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Babnigg G, Jedrzejczak R, Nocek B, Stein A, Eschenfeldt W, Stols L, Marshall N, Weger A, Wu R, Donnelly M, Joachimiak A. Gene selection and cloning approaches for co-expression and production of recombinant protein-protein complexes. ACTA ACUST UNITED AC 2015; 16:113-28. [PMID: 26671275 DOI: 10.1007/s10969-015-9200-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/27/2015] [Indexed: 10/22/2022]
Abstract
Multiprotein complexes play essential roles in all cells and X-ray crystallography can provide unparalleled insight into their structure and function. Many of these complexes are believed to be sufficiently stable for structural biology studies, but the production of protein-protein complexes using recombinant technologies is still labor-intensive. We have explored several strategies for the identification and cloning of heterodimers and heterotrimers that are compatible with the high-throughput (HTP) structural biology pipeline developed for single proteins. Two approaches are presented and compared which resulted in co-expression of paired genes from a single expression vector. Native operons encoding predicted interacting proteins were selected from a repertoire of genomes, and cloned directly to expression vector. In an alternative approach, Helicobacter pylori proteins predicted to interact strongly were cloned, each associated with translational control elements, then linked into an artificial operon. Proteins were then expressed and purified by standard HTP protocols, resulting to date in the structure determination of two H. pylori complexes.
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Affiliation(s)
- György Babnigg
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA.
| | - Robert Jedrzejczak
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Boguslaw Nocek
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Adam Stein
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - William Eschenfeldt
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Lucy Stols
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Norman Marshall
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Alicia Weger
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Ruiying Wu
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Mark Donnelly
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA.
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Tan K, Johnson PM, Stols L, Boubion B, Eschenfeldt W, Babnigg G, Hayes CS, Joachimiak A, Goulding CW. The structure of a contact-dependent growth-inhibition (CDI) immunity protein from Neisseria meningitidis MC58. Acta Crystallogr F Struct Biol Commun 2015; 71:702-9. [PMID: 26057799 PMCID: PMC4461334 DOI: 10.1107/s2053230x15006585] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 03/31/2015] [Indexed: 01/01/2023] Open
Abstract
Contact-dependent growth inhibition (CDI) is an important mechanism of intercellular competition between neighboring Gram-negative bacteria. CDI systems encode large surface-exposed CdiA effector proteins that carry a variety of C-terminal toxin domains (CdiA-CTs). All CDI(+) bacteria also produce CdiI immunity proteins that specifically bind to the cognate CdiA-CT and neutralize its toxin activity to prevent auto-inhibition. Here, the X-ray crystal structure of a CdiI immunity protein from Neisseria meningitidis MC58 is presented at 1.45 Å resolution. The CdiI protein has structural homology to the Whirly family of RNA-binding proteins, but appears to lack the characteristic nucleic acid-binding motif of this family. Sequence homology suggests that the cognate CdiA-CT is related to the eukaryotic EndoU family of RNA-processing enzymes. A homology model is presented of the CdiA-CT based on the structure of the XendoU nuclease from Xenopus laevis. Molecular-docking simulations predict that the CdiA-CT toxin active site is occluded upon binding to the CdiI immunity protein. Together, these observations suggest that the immunity protein neutralizes toxin activity by preventing access to RNA substrates.
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Affiliation(s)
- Kemin Tan
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA
- Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Parker M. Johnson
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Lucy Stols
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Bryan Boubion
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA
| | - William Eschenfeldt
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Gyorgy Babnigg
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Christopher S. Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Biomolecular Science and Engineering Program, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Andrezj Joachimiak
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA
- Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Celia W. Goulding
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA 92697, USA
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Nusca TD, Kim Y, Maltseva N, Lee JY, Eschenfeldt W, Stols L, Schofield MM, Scaglione JB, Dixon SD, Oves-Costales D, Challis GL, Hanna PC, Pfleger BF, Joachimiak A, Sherman DH. Functional and structural analysis of the siderophore synthetase AsbB through reconstitution of the petrobactin biosynthetic pathway from Bacillus anthracis. J Biol Chem 2012; 287:16058-72. [PMID: 22408253 PMCID: PMC3346087 DOI: 10.1074/jbc.m112.359349] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Indexed: 01/03/2023] Open
Abstract
Petrobactin, a mixed catechol-carboxylate siderophore, is required for full virulence of Bacillus anthracis, the causative agent of anthrax. The asbABCDEF operon encodes the biosynthetic machinery for this secondary metabolite. Here, we show that the function of five gene products encoded by the asb operon is necessary and sufficient for conversion of endogenous precursors to petrobactin using an in vitro system. In this pathway, the siderophore synthetase AsbB catalyzes formation of amide bonds crucial for petrobactin assembly through use of biosynthetic intermediates, as opposed to primary metabolites, as carboxylate donors. In solving the crystal structure of the B. anthracis siderophore biosynthesis protein B (AsbB), we disclose a three-dimensional model of a nonribosomal peptide synthetase-independent siderophore (NIS) synthetase. Structural characteristics provide new insight into how this bifunctional condensing enzyme can bind and adenylate multiple citrate-containing substrates followed by incorporation of both natural and unnatural polyamine nucleophiles. This activity enables formation of multiple end-stage products leading to final assembly of petrobactin. Subsequent enzymatic assays with the nonribosomal peptide synthetase-like AsbC, AsbD, and AsbE polypeptides show that the alternative products of AsbB are further converted to petrobactin, verifying previously proposed convergent routes to formation of this siderophore. These studies identify potential therapeutic targets to halt deadly infections caused by B. anthracis and other pathogenic bacteria and suggest new avenues for the chemoenzymatic synthesis of novel compounds.
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Affiliation(s)
- Tyler D. Nusca
- From the Life Sciences Institute and
- the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Youngchang Kim
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Natalia Maltseva
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | | | - William Eschenfeldt
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Lucy Stols
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | | | | | - Shandee D. Dixon
- the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Daniel Oves-Costales
- the Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Gregory L. Challis
- the Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Philip C. Hanna
- the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Brian F. Pfleger
- From the Life Sciences Institute and
- the Department of Chemical and Biological Engineering, University of Wisconsin, Madison, Wisconsin 53706-1691
| | - Andrzej Joachimiak
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
- the Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, and
| | - David H. Sherman
- From the Life Sciences Institute and
- the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
- the Departments of Medicinal Chemistry and Chemistry, University of Michigan, Arbor, Michigan 48109
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